J'ai un petit soucis, mon SMP Linux me fait des choses étranges, vus la discution d'hier, je ne sais pas où poster
[22:13:24] Completed 17500 out of 250000 steps (7%)
[22:25:29] Completed 20000 out of 250000 steps (8%)
[22:37:29] Completed 22500 out of 250000 steps (9%)
t = 49046.582 ps: Water molecule starting at atom 24859 can not be settled.
Check for bad contacts and/or reduce the timestep.
t = 49046.582 ps: Water molecule starting at atom 25216 can not be settled.
Check for bad contacts and/or reduce the timestep.
t = 49046.584 ps: Water molecule starting at atom 44212 can not be settled.
Check for bad contacts and/or reduce the timestep.
t = 49046.586 ps: Water molecule starting at atom 44212 can not be settled.
Check for bad contacts and/or reduce the timestep.
t = 49046.586 ps: Water molecule starting at atom 25216 can not be settled.
Check for bad contacts and/or reduce the timestep.
t = 49046.588 ps: Water molecule starting at atom 32209 can not be settled.
Check for bad contacts and/or reduce the timestep.
t = 49046.588 ps: Water molecule starting at atom 31837 can not be settled.
Check for bad contacts and/or reduce the timestep.
-------------------------------------------------------
Program mdrun, VERSION 4.0.99_development_20090307
Source code file: nsgrid.c, line: 357
Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.
Variable ci has value -2147483485. It should have been within [ 0 .. 2601 ]
For more information and tips for trouble shooting please check the GROMACS Wiki at
[url="http://wiki.gromacs.org/index.php/Errors"]http://wiki.gromacs.org/index.php/Errors[/url]
-------------------------------------------------------
Thanx for Using GROMACS - Have a Nice Day
Error on node 1, will try to stop all the nodes
Halting parallel program mdrun on CPU 1 out of 4
gcq#0: Thanx for Using GROMACS - Have a Nice Day
[cli_1]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 1
-------------------------------------------------------
Program mdrun, VERSION 4.0.99_development_20090307
Source code file: nsgrid.c, line: 357
Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.
Variable ci has value -2147483503. It should have been within [ 0 .. 2025 ]
For more information and tips for trouble shooting please check the GROMACS Wiki at
[url="http://wiki.gromacs.org/index.php/Errors"]http://wiki.gromacs.org/index.php/Errors[/url]
-------------------------------------------------------
Thanx for Using GROMACS - Have a Nice Day
-------------------------------------------------------
Program mdrun, VERSION 4.0.99_development_20090307
Source code file: nsgrid.c, line: 357
Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.
Variable ci has value -2147483539. It should have been within [ 0 .. 1734 ]
For more information and tips for trouble shooting please check the GROMACS Wiki at
[url="http://wiki.gromacs.org/index.php/Errors"]http://wiki.gromacs.org/index.php/Errors[/url]
-------------------------------------------------------
Thanx for Using GROMACS - Have a Nice Day
Error on node 2, will try to stop all the nodes
Halting parallel program mdrun on CPU 2 out of 4
gcq#0: Thanx for Using GROMACS - Have a Nice Day
[cli_2]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 2
Error on node 3, will try to stop all the nodes
Halting parallel program mdrun on CPU 3 out of 4
gcq#0: Thanx for Using GROMACS - Have a Nice Day
[cli_3]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 3
[22:41:19]
[22:41:19] Folding@home Core Shutdown: INTERRUPTED
[cli_0]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 102) - process 0
[22:41:23] CoreStatus = FF (255)
[22:41:23] Sending work to server
[22:41:23] Project: 2669 (Run 16, Clone 72, Gen 98)
[22:41:23] - Error: Could not get length of results file work/wuresults_02.dat
[22:41:23] - Error: Could not read unit 02 file. Removing from queue.
[22:41:23] Trying to send all finished work units
[22:41:23] + No unsent completed units remaining.
[22:41:23] - Preparing to get new work unit...
[22:41:23] + Attempting to get work packet
[22:41:23] - Will indicate memory of 1288 MB
[22:41:23] - Connecting to assignment server
[22:41:23] Connecting to [url="http://assign.stanford.edu:8080/"]http://assign.stanford.edu:8080/[/url]
[22:41:25] Posted data.
[22:41:25] Initial: 40AB; - Successful: assigned to (171.64.65.56).
[22:41:25] + News From Folding@Home: Welcome to Folding@Home
[22:41:25] Loaded queue successfully.
[22:41:25] Connecting to [url="http://171.64.65.56:8080/"]http://171.64.65.56:8080/[/url]
[22:41:33] Posted data.
[22:41:33] Initial: 0000; - Receiving payload (expected size: 4845500)
[22:41:58] - Downloaded at ~189 kB/s
[22:41:58] - Averaged speed for that direction ~181 kB/s
[22:41:58] + Received work.
[22:41:59] Trying to send all finished work units
[22:41:59] + No unsent completed units remaining.
[22:41:59] + Closed connections
[22:42:04]
[22:42:04] + Processing work unit
[22:42:04] At least 4 processors must be requested.Core required: FahCore_a2.exe
[22:42:04] Core found.
[22:42:04] Working on queue slot 03 [May 6 22:42:04 UTC]
[22:42:04] + Working ...
[22:42:04] - Calling './mpiexec -np 4 -host 127.0.0.1 ./FahCore_a2.exe -dir work/ -suffix 03 -checkpoint 5
-verbose -lifeline 5364 -version 624'
[22:42:04]
[22:42:04] *------------------------------*
[22:42:04] Folding@Home Gromacs SMP Core
[22:42:04] Version 2.07 (Sun Apr 19 14:51:09 PDT 2009)
[22:42:04]
[22:42:04] Preparing to commence simulation
[22:42:04] - Ensuring status. Please wait.
[22:42:05] Called DecompressByteArray: compressed_data_size=4844988 data_size=24001453,
decompressed_data_size=24001453 diff=0
[22:42:05] - Digital signature verified
[22:42:05]
[22:42:05] Project: 2675 (Run 0, Clone 2, Gen 125)
[22:42:05]
[22:42:05] Assembly optimizations on if available.
[22:42:05] Entering M.D.
[22:42:15] (Run 0, Clone 2, Gen 125)
[22:42:15]
[22:42:15] Entering M.D.
NNODES=4, MYRANK=0, HOSTNAME=virtu-desktop
NNODES=4, MYRANK=3, HOSTNAME=virtu-desktop
NNODES=4, MYRANK=1, HOSTNAME=virtu-desktop
NNODES=4, MYRANK=2, HOSTNAME=virtu-desktop
NODEID=3 argc=20
NODEID=2 argc=20
NODEID=0 argc=20
NODEID=1 argc=20
G R O M A C S (-:
Groningen Machine for Chemical Simulation
VERSION 4.0.99_development_20090307 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright © 1991-2000, University of Groningen, The Netherlands.
Copyright © 2001-2008, The GROMACS development team,
check out [url="http://www.gromacs.org"]http://www.gromacs.org[/url] for more information.
mdrun (-:
Reading file work/wudata_03.tpr, VERSION 3.3.99_development_20070618 (single precision)
Note: tpx file_version 48, software version 64
NOTE: The tpr file used for this simulation is in an old format, for less memory usage and possibly more performance
create a new tpr file with an up to date version of grompp
Making 1D domain decomposition 1 x 1 x 4
starting mdrun '22878 system in water'
31500000 steps, 63000.0 ps (continuing from step 31250000, 62500.0 ps).
[22:42:25] Completed 0 out of 250000 steps (0%)
[22:54:30] Completed 2500 out of 250000 steps (1%)
[23:06:42] Completed 5000 out of 250000 steps (2%)
[23:18:54] Completed 7500 out of 250000 steps (3%)
Quelqu'un peu me dire ce que je dois faire ? Où est-ce un bug du core_a2
Merci
Edit: Pourquoi la codebox est si grande
